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- PDB-3huj: Crystal structure of human CD1d-alpha-Galactosylceramide in compl... -

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Basic information

Entry
Database: PDB / ID: 3huj
TitleCrystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor
Components
  • (NKT15 T cell receptor ...) x 2
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1d
KeywordsIMMUNE SYSTEM / CD1d / NKT T cell receptor / alpha-galactosylceramide / protein receptor complex / Cell membrane / Disulfide bond / Endosome / Glycoprotein / Host-virus interaction / Immune response / Immunoglobulin domain / Innate immunity / Lysosome / Membrane / Transmembrane / Disease mutation / Glycation / MHC I / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / detection of bacterium / cell adhesion molecule binding / positive regulation of T cell proliferation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AGH / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPang, S.S.
CitationJournal: Immunity / Year: 2009
Title: Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors
Authors: Pellicci, D.G. / Patel, O. / Kjer-Nielsen, L. / Pang, S.S. / Sullivan, L.C. / Kyparissoudis, K. / Brooks, A.G. / Reid, H.H. / Gras, S. / Lucet, I.S. / Koh, R. / Smyth, M.J. / Mallevaey, T. / ...Authors: Pellicci, D.G. / Patel, O. / Kjer-Nielsen, L. / Pang, S.S. / Sullivan, L.C. / Kyparissoudis, K. / Brooks, A.G. / Reid, H.H. / Gras, S. / Lucet, I.S. / Koh, R. / Smyth, M.J. / Mallevaey, T. / Matsuda, J.L. / Gapin, L. / McCluskey, J. / Godfrey, D.I. / Rossjohn, J.
History
DepositionJun 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1d
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1d
D: Beta-2-microglobulin
E: NKT15 T cell receptor alpha-chain
F: NKT15 T cell receptor beta-chain
G: NKT15 T cell receptor alpha-chain
H: NKT15 T cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,82015
Polymers190,6678
Non-polymers3,1537
Water8,683482
1
A: T-cell surface glycoprotein CD1d
B: Beta-2-microglobulin
G: NKT15 T cell receptor alpha-chain
H: NKT15 T cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8218
Polymers95,3334
Non-polymers1,4874
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-cell surface glycoprotein CD1d
D: Beta-2-microglobulin
E: NKT15 T cell receptor alpha-chain
F: NKT15 T cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9997
Polymers95,3334
Non-polymers1,6663
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.112, 82.360, 117.184
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11H-268-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein T-cell surface glycoprotein CD1d / R3G1


Mass: 32324.383 Da / Num. of mol.: 2 / Fragment: UNP residues 21-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Cell line (production host): High-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

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NKT15 T cell receptor ... , 2 types, 4 molecules EGFH

#3: Protein NKT15 T cell receptor alpha-chain


Mass: 23227.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein NKT15 T cell receptor beta-chain


Mass: 28033.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 4 types, 6 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9

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Non-polymers , 2 types, 483 molecules

#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNO SUITABLE DATABASE REFERENCES WERE FOUND FOR CHAINS E, F, G AND H.(KJER-NIELSEN, L., BORG, N.A., ...NO SUITABLE DATABASE REFERENCES WERE FOUND FOR CHAINS E, F, G AND H.(KJER-NIELSEN, L., BORG, N.A., ET AL., J. EXP MED. 203(3) 661-673), 2006

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris-HCl, 0.2M magnesium chloride, 12% PEG 10000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 66054 / Num. obs: 66054 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5344 / % possible all: 74.3

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Processing

Software
NameVersionClassification
Blu-IceGUI (SSRL)data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2po6

2po6


Resolution: 2.5→47.28 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.876 / SU B: 21.082 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.762 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27883 3288 5 %RANDOM
Rwork0.21595 ---
all0.21912 62421 --
obs0.21912 62421 90.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.92 Å2
2--0 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12944 0 213 482 13639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02113582
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.94718484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64651630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04424.022634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.474152124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0841577
X-RAY DIFFRACTIONr_chiral_restr0.0730.22009
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210347
X-RAY DIFFRACTIONr_nbd_refined0.1890.25660
X-RAY DIFFRACTIONr_nbtor_refined0.30.28938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2804
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.222
X-RAY DIFFRACTIONr_mcbond_it0.371.58388
X-RAY DIFFRACTIONr_mcangle_it0.657213216
X-RAY DIFFRACTIONr_scbond_it0.7736027
X-RAY DIFFRACTIONr_scangle_it1.2464.55268
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 186 -
Rwork0.292 --
obs-3763 70.92 %

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